The design, synthesis, and evaluation of a series of CC-1065 and duocarmycin analogues are described in efforts to define fundamental relationships between structure, reactivity, and biological properties. These include deep-seated structural changes in the DMAalkylation subunits, the exploration of a novel series of alkylation subunit DMAcross-linking analogues, and an examination of altered DMAbinding subunits. Each of these modifications or approaches is used to address a specific question or concept relating structure and function (structure-reactivity or structure-activity). Central to these studies is the use of organic synthesis and fundamental physical organic principles to define the underlying recognition features responsible for the sequence selective DMAalkylation reaction and its source of catalysis. Through these studies, we hope to fully characterize the first well-defined example of a new mechanism of in situ activation of a DMA alkylating antitumor agent and the first example of activation at and by the biological target. The introduction and continued development of new techniques for establishing DMAbinding selectivity and affinity promises to facilitate these and related studies and are being extended to include the inhibiton of aberrant gene transcription. Public Health Relevance: New drugs for the treatment of cancer will be explored and new general concepts of drug design may emerge from the investigations.